Variation in Ensembl Chromosome ID
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4.8 years ago
Mel ▴ 60

Hi, I've been parsing through some Ensembl CDS files (using BioPython), and I'm getting some variation in how the chromosome ID is specified. Typically it is specified like this: "chromosome:GRCh38:7:142786213:142786224:1". However, other times it is specified like this: 'chromosome:GRCh38:CHR_HSCHR7_2_CTG6:142847306:142847317:1'. Why is this variation present? What does 'CHR_HSCHR7_2_CTG6' specify exactly? Thanks for any clarification or help.

genome • 858 views
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4.8 years ago
JC 13k

That is a haplotype sequence, check https://www.ensembl.org/Help/Faq?id=291 for more information

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Excellent! Thank you JC!

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